Tuesday, November 24, 2009

For those of you who only know him as a paleontological researcher, Scott is also a very skilled communicator and educator. The past few months have seen some tremendous successes in that regard - first, his on-screen and behind-the-scenes role with the new PBS kids' show Dinosaur Train, and second, his just-published book Dinosaur Odyssey.

Scott has a special interest in popularizing issues of science education, evolution, sustainability, and paleontology, all of which promise to be themes on the new blog. This will be a good one to add to your regular reading list!

Monday, November 16, 2009

In the spirit of some earlierposts on this blog, The Scholarly Kitchen (an excellent blog for those interested in following issues of open access publishing) has this post about the utility of ratings systems at journals such as PLoS ONE. Interesting food for thought.

Geoscientists impact our lives in more ways than most of us realize. Did you drink a glass of clean water this morning? Geologists and hydrologists help to keep our water supply clean and safe. Did you fill your car with gas this week? A petroleum geologist helped locate the oil deposits and coordinate their extraction. Do you use a cell phone or laptop? The cobalt in the batteries (and nearly all of the other raw materials) was mined from deposits located by geologists. Did your local roads not wash away during the last major rainstorm? A geologist likely had a role in that too. Not to mention all of the paleontologists, planetary geologists, sedimentologists, mining engineers, and the like who have significant training in geology departments around the world.

Surveys find that we are facing a severe shortage of trained geoscientists in the coming decades, as the older generations retire. Our need for geoscientists is not going away, and closing geology departments is not a way to rectify this.

What can you do? Check out these twoposts by Chris Noto (guesting at ReBecca's Hunt's Dinochick Blogs) for more information. Don't let the MSU geology department go extinct!

Wednesday, November 11, 2009

Many of the recent posts on this blog have dealt with issues of access to the scholarly literature for those outside the library systems of large research institutions. A digital divide is developing in academia, largely due to the expensive costs of institutional subscriptions and pay-per-download distribution schemes of commercial and non-profit publishers alike.

Thus, I was very excited to hear about the launch of DeepDyve. This website essentially offers a rental service for scholarly publications. Search a database, find an article, and view it on the website's Flash viewer. The prices are quite reasonable - 99 cents per article for the Basic Plan, $9.99/month to get 20 rentals a month on the Silver Plan, and $19.99/month to get unlimited rentals on the Gold Plan. I decided to test out a free trial of the Gold Plan and see if DeepDyve was right for me.

Promotional literature promised "30 million articles from thousands of authoritative journals," so I was expecting good things. Landing on DeepDyve's simple, attractive home page, I sat down to run my first queries.

Unfortunately, the hype hasn't yet caught up with the reality of scholarly publishing. A search for "Triceratops" launched from the web site's home page generated over 84,000 hits. . .most of which were completely irrelevant medical literature ("Median and Radial Nerve Compression About the Elbow" popped up on the first page, for instance). Using the site's advanced search filters, I was able to trim the results down to 71 articles. Of these articles, 8 were listed as "free" (they were already available through open access journals) and 61 only offered a preview of the abstract. A scant 2 articles were available for rental (from the journals Annual Review of Earth and Planetary Sciences and Annual Review of Ecology and Systematics).

Why such a poor showing? It comes down to the fact that many of the societies and publishers that own or license our publications haven't yet reached an agreement with DeepDyve to allow rental of relevant articles. Thus, papers from heavy hitters like Journal of Vertebrate Paleontology and Paleobiology simply aren't available.

The rental plan also may turn some people off (although I don't think it is a complete deal breaker). In short, you can't download a PDF - all you can do is look at the file within the provided viewer. This is useful for those times when the article turns out to be irrelevant. But, it may ultimately prove unsatisfactory for those inevitable moments when you want to be able to access literature away from an internet connection (and we all have those times!). And, it seems somewhat unsettling to pay for content that you don't actually get to keep (unlike services such as iTunes).

I want to like DeepDyve. . .I really do! It promises to open up swaths of the scholarly literature that were previously unavailable. But, right now DeepDyve is shackled by the limited availability of publications (at least for us paleontologists). There is very little value-added over a standard Google search. Perhaps the future has big things in store. . .I'll be keeping an eye on the situation!

For additional commentary on DeepDyve, and some responses from the company, check out this post at the Scholarly Kitchen.

Tuesday, November 10, 2009

On a personal note, I have recently stepped up as "Section Editor" for paleontology at PLoS ONE. This means that I'll be coordinating the editorial flow for most paleo-themed papers that come the journal's way.

One of the real joys of editing fora major journal like PLoS ONE is getting a "sneak peak" at some pretty nifty research. Today, Herman Pontzer, Vivian Allen, and John Hutchinson have a new paper that should be of interest to this blog's general audience [full disclosure: I was the academic editor for this contribution]. As always, papers at PLoS ONE are free to download, comment upon, and rate.

AbstractBackgroundOne of the great unresolved controversies in paleobiology is whether extinct dinosaurs were endothermic, ectothermic, or some combination thereof, and when endothermy first evolved in the lineage leading to birds. Although it is well established that high, sustained growth rates and, presumably, high activity levels are ancestral for dinosaurs and pterosaurs (clade Ornithodira), other independent lines of evidence for high metabolic rates, locomotor costs, or endothermy are needed. For example, some studies have suggested that, because large dinosaurs may have been homeothermic due to their size alone and could have had heat loss problems, ectothermy would be a more plausible metabolic strategy for such animals.

Methodology/Principal FindingsHere we describe two new biomechanical approaches for reconstructing the metabolic rate of 14 extinct bipedal dinosauriforms during walking and running. These methods, well validated for extant animals, indicate that during walking and slow running the metabolic rate of at least the larger extinct dinosaurs exceeded the maximum aerobic capabilities of modern ectotherms, falling instead within the range of modern birds and mammals. Estimated metabolic rates for smaller dinosaurs are more ambiguous, but generally approach or exceed the ectotherm boundary.

Conclusions/SignificanceOur results support the hypothesis that endothermy was widespread in at least larger non-avian dinosaurs. It was plausibly ancestral for all dinosauriforms (perhaps Ornithodira), but this is perhaps more strongly indicated by high growth rates than by locomotor costs. The polarity of the evolution of endothermy indicates that rapid growth, insulation, erect postures, and perhaps aerobic power predated advanced “avian” lung structure and high locomotor costs.

In my last post, I required you readers to publicly shame me if I didn't get right to work on my contributions. Well, I deserve to be shamed. I will confess to doing virtually nothing over the last few weeks (aside from a few very, very minor edits). . .thus, setting a very, very bad example. (although I did help get another manuscript that's not part of the challenge into review!)

Thursday, October 29, 2009

On-line journals are great. You get immediate access to the latest research and can download a fully searchable PDF for later use. Journal digitization has revolutionized the pace of science communication and increased the reach of formerly obscure journals. Through the wonders of the Internet, anyone can get access! Right?

Not so fast. On-line journals offer full benefits only to those whose institution has a subscription. If you don't have a subscription, you're out of luck. . .mostly. Thankfully, it is possible to buy PDFs of individual articles. Right?

Not so fast. It is indeed possible to buy PDFs of articles from most journals. . .if you can cough up the money to do so. Let's face it. PDFs are expensive. Ridiculously so. A three page note from Journal of Vertebrate Paleontology might cost nearly $30! A six page paper from Geology runs $25. [end of this post] Is it really worth it?

Big ProblemsI won't pretend that journal sales don't support professional societies I care about. I won't pretend that publishers shouldn't get compensated for their services. I won't pretend that everything is going to turn open access tomorrow.

But, I'm not shy about saying that the current system stinks. No matter how you slice it, $30 for a PDF article is unaffordable for a typical consumer of paleontological publications. The new membership rates for the Society of Vertebrate Paleontology, which include electronic access to Journal of Vertebrate Paleontology, cost $115 for e-journal only. Assuming around 120 articles per year (a rough count for JVP in 2008), this works out to a little less than $1 per article (and remember that this assumes that 100 percent of membership dues go to the journal subscription - certainly not the case). Why is there a 3,000 percent markup for non-members? Wouldn't journals be able to get by with, perhaps, a 500 percent markup over the member rate? [IMPORTANT NOTE: I am not intending to single out JVP and SVP exclusively; nearly all journal publishers are guilty of this problem. . .it just so happens that JVP is the example most relevant to most readers here]

Let's put it another way. At the current costs of PDF articles, buying every single article in the journal would cost an individual around $3,600 per year.

And let's look at it from yet another angle. Institutional paper subscriptions to JVP are $270/year for US institutions (pre-Taylor & Francis switch; we don't yet know what the cost will be post-switch). This works out to an average of$2.25/article. . .for a format that is much more expensive to deliver than an electronic document!

And one last angle. . .the Mesozoic Birds: Above the Heads of Dinosaurs edited volume, which is a beautifully produced and scientifically important work, includes 20 articles, ships in hard cover and retails for $100 new. This works out to $5/article within the book. Contrast this with $30 or more for a single digital file.

Commenting in a recent thread here at the OSP, a librarian noted that libraries are paying between $2-$4 per PDF article when bought in bundles from for-profit publishers like Elsevier (which, incidentally, continues to post profits in the midst of the recession). Although it is certainly fair to have volume discounts (although the pricing schemes and the bundled journals are often rather dubious in practice), it is of dubious benefit to science to charge such a disproportionate rate to private individuals who are just trying to do some science.

Do these pricing schemes serve science? Do these pricing schemes serve the interests of the authors, who just want their work to be read?

Commonly Suggested "Solutions"When the issue of paying for individual PDFs is brought up, there are often a number of "solutions" proposed. I put the word in quotes because, as explained below, none of these is fool-proof.

Why not write the author for a PDF?In some cases, this is a good workaround. But it's never a perfect workaround. Sometimes authors are unresponsive, have changed email addresses, retired, or passed into the fossil record. In this case, the researcher in need of the paper is out of luck.

Why not post a PDF request to VRTPALEO or the DML?In some cases, this is a workaround. . .one need only look at mailing list archives to see that this is a common strategy. But, PDF requests unfortunately carry a small annoyance factor for many list subscribers. Sometimes no one responds. Finally, PDF sharing by anyone other than the author is generally illegal in the eyes of the publishers and societies (but let's not pretend it doesn't happen).

Why not join the society, and then you get all of the articles as part of your membership?Again, this is a solution in some cases. If you are a paleontological enthusiast or professional who loves (or needs) to follow every bit of the literature, you should probably join the Society of Vertebrate Paleontology and/or the Palaeontological Association and/or the Paleontological Society.

But, let's be realistic. Nobody can afford to join every society to get access to all society publications. In some cases, it's just not necessary. Consider this hypothetical situation. You're a population biologist working for a small nature preserve who wants a little background on the evolutionary history of the coyote. You do a search on Google, and find a citation to Journal of American Paleontology with an abstract that details ecological shifts by coyotes during the Ice Age using isotopic analysis. You click on the link, and. . .paywall! The Society of American Paleontology wants $30 for a five page article. Is it really worth your time and money (as a population biologist) to join a society of paleontology, when you are already stretching your budget to cover dues for two more relevant societies? If the charter for the American Paleontological Society says that they are to promote and advance the science of paleontology, is the society really living up to this mandate? If the society wants to foster cross-discipline appreciation for the relevance of the field, is this happening if the research is not easily accessible? Are the authors who contribute to the journal being well-served by having their research so restricted?

Finally, some journals just aren't sponsored by societies. There is no solution in this case, other than to pay a few hundred dollars per year.

Most of the other journals charge $30 for a PDF!This is not a solution (or even a "solution"), but an excuse. During the business meeting for a scholarly society to which I belong, I raised a concern about the prices that the society's journal was charging for individual PDFs. Can you guess the answer that I received? I remember something my mother often said to me. . ."If everyone else jumped off a cliff, would you too?" Exorbitant PDF costs may be the norm, but that doesn't mean it's the ethical thing to do (especially for a non-profit society whose stated mission includes phrases like "advance the science" and "serve the common interests").

What Needs to Change?Science (yes, that's the reason why most research is published) is not being served by the current pricing schemes. Alleged solutions for those beyond the boundaries of the pay-wall are not comprehensive, and again do not serve the interests of science.

PDFs of individual articles need to cost less. There is no way to legitimize charging $25, $30, or more for something that costs less to produce than a printed journal, particularly when it prices out to up to a 3,000 percent markup. The current pricing scheme restricts the readership of articles and creates a hierarchy of have- and have-not researchers, in a time when the Internet is supposed to fix these problems for academia. Also, let's not forget that the research behind these articles is often heavily subsidized by public tax dollars. . .

I would suggest that $5, or maybe $10 in exceptional circumstances (e.g., a 50 page monograph) is a cost that I would be willing to pay for a PDF. I would also submit that many journals would see increased PDF sales (particularly for popular topics, such as dinosaurs) if the price was set at something mere mortals could afford to pay.

Is There a Solution?Right now, it sounds like I'm doing a lot of complaining and not a lot of problem solving. Well. . .yes. This post is partly a rant. Unless people are aware of the problem, nothing will ever happen.

So what can we do? Here are a few suggestions:

Ask journals and professional societies to consider the implications of pricing schemes for PDFs. Speak out to the people who matter. Let them know how you feel, and how it affects you.

Submit your work only to journals with researcher-friendly publishing policies.

If you are an author, do everything you (legally) can to get your work out there for free. If the journal allows you to post a PDF, do so. Respond promptly to PDF requests from other individuals.

What are your thoughts?

Addendum 1: As if by magic, this post at The Scholarly Kitchen appeared at nearly the same instant as I hit the "publish" button on this post. I haven't followed up on the service (which essentially offers cheap rental access to articles from various scientific publishers), but will certainly be looking into it.

Wednesday, October 28, 2009

Distinguishing the skulls of juveniles and adults of the same species, and sometimes different species, can be a prickly thing in the fossil record. The result is that paleontology is littered with juvenile fossils that have been considered adults at some time or another. The crested duck-billed dinosaur Corythosaurushas also been known under names like Procheneosaurus, the famous Monocloniusis actually a juvenile of adult Centrosaurus, Styracosaurus, and kin, and the debate still continues on whether Nanotyrannusis a juvenile Tyrannosaurus.

Yesterday in the open access journal PLoS ONE, paleontologists Jack Horner and Mark Goodwin published a long-awaited paper positing synonymy for a trio of iconic (and melodiously-named) dinosaurs. The bone-headed dinosaurs Pachycephalosaurus, Stygimoloch, and Dracorex are all one and the same animal, according to their work. The latter two are juvenile stages, whereas Pachycephalosaurus represents a full adult.

Skulls of Pachycephalosaurus (top), Stygimoloch (middle; the front of the skull is missing), and Dracorex (bottom; the skull is crushed from top to bottom). In particular, note the changes in skull size and similarities in spike placement. Modified after the original in Horner and Goodwin 2009.

How is this possible? The animals look so different, right? Pachycephalosaurus has this big bowling ball on top of its head, which the other two lack. Stygimoloch has a uniquely-shaped, narrow dome, and Dracorex has a completely flat head. Furthermore, Pachycephalosaurus lacks the elongated spikes that make the other two look so fearsome.

Well, it turns out that this can all be attributed to ontogenetic changes (i.e., change as the animals get older). Horner and Goodwin assemble multiple lines of evidence for this hypothesis.

First, the skulls of Dracorex, Stygimoloch, and Pachycephalosaurus form a size gradation from smallest to largest--exactly what one would expect for a growth series. By itself, this is not irrefutable proof, of course--it could just be that Dracorex had a small adult size compared to Pachycephalosaurus.

Second, many of the knobs and bumps on the skulls can be matched up one for one between individuals of the various specimens. Alternatively, one would also expect that closely related (but different) species might have similar patterns of bumps. As Horner and Goodwin admit, there is some variation between individuals of the different "species"--but, the authors also note that this sort of variation is entirely expected and occurs even within undisputed adult Pachycephalosaurus.

Third, specimens of Stygimoloch, both in CT scans and physically cut specimens, show an open suture between the two frontal bones of the dome. Pachycephalosaurus domes are completely fused up. Open sutures are often strong indications that an animal is still growing--and, it's particularly intriguing that a small "species" has them but a large "species" doesn't!

Finally, microscopic examination of the bones in two of the three "species" (Stygimoloch and Pachycephalosaurus; there weren't any Dracorex available for cutting up) shows that Stygimoloch was still growing (and thus not a full adult)--but Pachycephalosaurus specimens weren't growing much at all (and therefore were probably full adults).

Any one of these lines of evidence might be interesting, but not completely convincing. Taken together, however, they make a pretty compelling case that Dracorex and Stygimoloch are juvenile Pachycephalosaurus. Because Pachycephalosaurus was named first, the first two become junior synonyms. It's a shame, because they're such cool names!

As for duckbilled dinosaurs, horned dinosaurs, and even modern crested birds like the cassowary, the story in the pachycephalosaurs suggests that weird ornaments on the skull were something that happened only as the animals approached full size. The domes practically appeared overnight! The teenage years must have been a real headache for these dinosaurs.

Thanks to the wonders of open access, the article is freely available for all to read. Additionally, it is worth taking advantage of the rating and comment features at PLoS ONE [disclaimer: I am a section editor for that journal]. . .few other scientific publications allow the readers to annotate the papers directly!

Wednesday, October 21, 2009

I finally managed to publish in Nature (along with Mike Taylor and Matt Wedel)! Ok, it's only a glorified letter to the editor. But we still won't complain. Our contribution [subscription required; I know, it's ironic] focuses on the issue of data sharing in paleontology. It's partly a plea for greater data availability, and partly an advertisement for the Open Dinosaur Project. For more details, see my post at the ODP project blog.

Tuesday, October 20, 2009

Continuing with our Open Access Week theme, I wanted to highlight some previous posts on the issue here at the Open Source Paleontologist. In other words, I don't have time to write a more comprehensive post right now. So, enjoy these old ones!

Monday, October 19, 2009

October 19 - October 23 is designated Open Access Week, in order to raise awareness of open access publication and scholarship. So, I'll be blogging a little bit more about open access during the next few days.

For my first post, I wanted to clarify a common confusion that I hear from many colleagues: open source vs. open access. Although the terms are related in some ways (indeed, they derive from a very similar philosophy), they refer to two discrete concepts.

Of course, many questions remained for those of us who follow issues of academic publishing and access to publications. What would happen to copyright of articles? Who gets the profits from sales of the journal? Would authors still be able to post a PDF on their website? So, I drafted an email and sent it along to the relevant folks in SVP's leadership.

I am now happy to say that an extensive list of FAQs, responding to questions from me and other folks, is now posted at SVP's website [link to PDF]. Every single one of my questions (and others) was addressed, in detail. My sincere thanks goes to the individuals at SVP who put this together! Major points (and some commentary) follow:

CopyrightCopyright will stay with the Society of Vertebrate Paleontology (as appropriate - publications produced by many government workers should be exempted), as has been the case in the past. This is a Good Thing.

Is This Forever?The contract lasts five years - so, SVP has the option to find another publisher or renegotiate at the end of this period. Again, a Good Thing. This also means, however, that those society members with an interest in commenting on or influencing the renewal process have about three (or at most four) years to wait before springing to action. Mark your calendars for SVP 2012 and 2013. Given the rapid pace at which academic publishing is changing right now, it will certainly be worth taking a close look at the conditions of journal publication in a few years.

Author BenefitsIn the new publishing arrangement, authors will benefit from faster publication (by going from four issues a year to six). This is, of course, a major plus. Other benefits are, in my opinion, slightly more mixed. Gone are the days when we can (legally) pay an affordable fee for the right to post the PDF of our published work to a personal web page. We will, however, receive a PDF that can be emailed to colleagues and those who request it. This unfortunately represents a step backwards for the (legal) distribution of paleontological information. As a consolation prize, though, we get 50 free paper reprints of our articles! [editorial note: I had a rant written on this topic, but decided against including it here in the end. Suffice it to say that I personally find paper reprints less than useful in this day and age, recognizing that others may not share this opinion]

Open AccessIt is probably no surprise that JVP will not be going to an open access model, even a delayed open access model. On a small positive note, authors now have the option of purchasing complete open access for their article (presently, to the tune of $3,250) through Taylor & Francis's iOpenAccess program.

Final ThoughtsIt's still far too early to know for sure how JVP's transition to Taylor & Francis will work out. As mentioned above, the world of academic publishing is changing. Only time will tell if the switch is a Totally Good Thing or not.

Of course, what's the point of having a challenge without being challenged just a little bit? The whole point of this is to nudge. . .cajole. . .motivate. . .humiliate. . .all of us into finishing up those nagging papers. With less than three months to go, it's time to start kicking things into overdrive.

PPCers: Now it's time to make good on your promises. In the comments below, drop a note to tell us how you're doing! It's upon all of us to make each other finish these papers!

I'll start. I've committed to finishing a paper on a Myledaphus tooth site, as well as finish up revisions on one of my dissertation chapters. Right now, I'm ashamed to say that I haven't done a thing. But, the good news is that the dissertation chapter is on my priority list for the coming week. Readers: if I don't indicate any progress by Friday, you are allowed. . .nay, required. . .to publicly humiliate me. And while you're at it, get to work on your own papers!

In my casual internet browsing, I've noticed that a few of you have blogged about your efforts on the PPC (or at least mentioned them in passing). Here's a quick run-down of some of the links - once again, please let me know if I've left anyone out! And if you're a blogger, but haven't blogged about your participation, why not give it a try now?

Friday, October 2, 2009

In the event that you were trapped under a building for the past two weeks, the annual Society of Vertebrate Paleontology meetings have come and gone. Not only do these meetings provide a nice outlet for ongoing research, they also provided an opportunity for me and Dave to 1) recruit more participants for the Paleo Paper Challenge; and 2) nag everyone to get to work on their papers, already! With the SVP recruits and new volunteers from the comment threads of this blog, the Paleo Paper Challenge is rounding out nicely. Oh yeah, and I finally got to meet Dave Hone in person.

Thursday, October 1, 2009

I'm just back from SVP/associated collections visits, enjoying the post-SVP glow of research motivation as well as a big pile of things on my "to-do" list. Among these are an update of the Paleo Paper Challenge, commentary on the new Journal of Vertebrate Paleontology publication contract, and much more.

In the meantime, I wanted to call your attention to a whole blizzard of paleontology-relevant publications that have been unleashed from the on-line, open access journal PLoS ONE during the past two weeks. Although I'm an admittedly biased opinion (I am an academic editor for the journal), it is quite nice to see so many interesting and relevant paleontology publications within PLoS ONE's "pages." I am short on time, and many of these articles were covered in depth by other bloggers, so I'm just posting the references this time around.

The PapersArribas A, Garrido G, Viseras C, Soria JM, Pla S, et al. (2009) A Mammalian Lost World in Southwest Europe during the Late Pliocene. PLoS ONE 4(9): e7127. doi:10.1371/journal.pone.0007127

Wolff EDS, Salisbury SW, Horner JR, Varricchio DJ (2009) Common Avian Infection Plagued the Tyrant Dinosaurs. PLoS ONE 4(9): e7288. doi:10.1371/journal.pone.0007288 [Note--Ewan Wolff, the senior author on this paper, was my co-author on the "fighting Triceratops" paper that came out earlier this year. Nice to see more paleopathology stuff out there!]

Sunday, September 20, 2009

After ourposts issuing the Paleo Paper Challenge, we have had a number of very brave souls step up to the plate. We're dusting those old papers off of our hard drives, finishing them up, and making a commitment to get them through into review!

Of course, it wouldn't be a challenge if we weren't holding our feet to the fire with the possibility of public embarrassment. All of us have signed on the dotted line, and committed to getting these puppies out the door by January 1, 2010!

It's not too late to sign up yourself! There's always room for one more - so join the party!

Acceptors of the Paleo Paper Challenge

Tor Bertin:Manuscript on mystery specimen

Andy Farke:Myledaphus paperFinal dissertation chapter

John Foster:Unspecified paper

Casey Holliday:Articular cartilage paper

Dave Hone:Unspecified paper

ReBecca Hunt:Unspecified paper

Bill Parker:Revueltosaurus manuscript

Heinrich Mallison:Plateosaurus CAE (is waiting for the two other diss chapters to come out of review)sauropods rearingalligator muscle cross sectionsnon-Plateosaurus at MFN descriptionsauropodomorph rapid locomotion

Thursday, September 17, 2009

Writing papers is fun, but rather pointless unless anyone reads them, uses them, and cites them. How do we find out if anyone reads our work? Gross citation counts are nice, and easily provided by ISI Web of Science (easily, that is, if your institution coughs up the money to pay for the database) or Google Scholar (free, but not always as comprehensive as ISI's counts). These services also provide links to the papers with the citations. This is useful, but everyone knows that more people read the paper than actually cite it. The problem, of course, is that there is no way to know how many are reading the darned thing.

Until now. Public Library of Science (the publishers of PLoS ONE, PLoS Biology, and other open access journals; in the interests of full disclosure, I'm an academic editor for PLoS ONE) has just completely shifted the playing field. Free, article-level metrics are now available. Easily. With one click, you can find out how many page views a research article has had and how many people have downloaded the PDF. Better yet, you can track trends through time and download the data into an Excel spreadsheet for further analysis.

Just for fun, I checked out the stats for my co-authored paper on Triceratops horn use, which was published in January of this year. To date, the publication has had over 7,000 page views, 851 downloads of the PDF file, and 1 citation. The paper on Darwinius, which came out shortly after the Triceratops paper, has had over 66,000 page views and over 5,800 downloads of the PDF file. PLoS ONE also provides summary tables for selected disciplines - a paper on evolutionary biology (which includes paleontology, for most purposes) published in 2008 could expect to have racked up at least 2,200 hits by now.

So what's to like here? Well, an author gets an immediate sense if someone is paying attention to a publication. Page views and PDF downloads are a valuable tool for gauging community interest. In concert with citation data, it's probably a far better gauge of a paper's worth than the impact factor for the journal that the publication happens to show up in. The data are also freely available, transparent, and frequently updated. The latter is particularly important because it may be years before a paper's full impact is known. An open-access metric for an open-access world.

And are there any problems? As with any metric, the unfortunate answer is yes. Page view counts probably include a lot of casual readers, who read the abstract and promptly forget the existence of the article in question. These counts could also be gamed by "click contests" - one need only smell the stench emanating from the hordes of Pharyngula's zombie fanboyz as they lurch towards the next on-line poll to realize just how malleable page view data potentially are (although to PLoS's credit, they have attempted to filter out any robot and web crawler traffic). The metric will also be abused by administrators, who will still make career-ending decisions based on a number (although at least it's a hopefully more relevant number this time). Once again to PLoS's credit, they provide explanatory and cautionary pages candidly outlining the pros and cons of the metric.

I suspect that other journals will follow suit - it may not happen tomorrow, but it will happen. We may be seeing the death of the traditional, sometimes tyrannical, "impact factor." Let's hope we don't replace it with a new despot!

Monday, September 14, 2009

Dave Hone of Archosaur Musings and I were recently chatting online and were lamenting the inevitable problem of ‘the unfinished paper’. Most researchers have a project or two (or anything up to 20) that were started and then kind of stalled for various reasons – uncooperative co-authors, being unable to find the elusive essential paper, other projects taking priority, or just general malaise. It’s left as a few pages of notes, or unreferenced, without figures or a key analysis complete or whatever. It’s good science and publishable, it’s just not done. Without a good incentive to get them finished off (like a rival group) or them getting out of date (the stuff is interesting but not ground breaking and will not revolutionize the field when it comes out, but it’s not old either) these things can last for ever. Sometimes, all the manuscript needs is one day of solid work to kick the thing out the door!

Both of us have these kinds of papers knocking around and we are far from the only ones. As such with SVP around the corner we decided to issue the Paleo Paper Challenge (or Palaeo Paper Challenge, if you're so inclined). If you have a palaeo paper that really needs to be finished off then we challenge you to sign up here and get it done this year. If so, simply leave a note in the comment thread and we’ll total them all up in a few days and create a register of those taking part (so you can’t back out!). There is no need to let everyone know exactly what it is you are working on (if people want to keep things private, that’s fine) but of course juicy details will be welcome. Dave and I will also both be canvassing at SVP, and if you want to encourage others to join, do please mention this on your own blogs etc.

This should serve as both self-motivation to get the project done and a nice little race to see who can finish first and get their paper(s) submitted or in print. The real challenge of course is simply to get it done, so we are setting January 1, 2010, as your ‘official’ deadline – if you are joining the challenge you’ll have about three months to get it done. There are hundreds if not thousands of these papers languishing on hard drives so let’s try and get a few of them out there!

[NOTE: This post was largely written by Dave. . .I've modified it slightly for posting here. Perhaps this laziness is why I have so many half-finished papers sitting on my hard drive right now.]

Monday, September 7, 2009

A few months ago, Matt Wedel (of SV-POW! fame) lamented the lack of measurements in most contemporary scientific papers. As a real numberhead, his post resonated with me. It got me thinking. Despite the shortcomings of some papers, there are a lot of measurements out there in the literature already. With measurements, you can do science. Potentially some really cool science. But how could I collect all of these data? This could take years!

The gears in my brain started turning. One idea led to another. A plan was forming. Something crazy. Deeply, insanely crazy.

So what happened next? I teamed up with SV-POW's Matt Wedel and Mike Taylor to create a research project in dinosaur paleontology that anyone can participate in. The Open Dinosaur Project. We (yes, "we" includes you) will comb through the literature (which, thanks to a number of open access publications and archives, is quite data-rich) and pull out measurements for further analysis. The process - from data collection to analysis to publication - will be completely open. Every step of the way will be blogged. And. . .all contributors are invited to join us as co-authors. The project: look at the evolution of the limbs in ornithischian dinosaurs.

Saturday, September 5, 2009

Research of catastrophic proportions. Another piece of the Shiny Digital Future. An unholy union between members of SV-POW! and The Open Source Paleontologist. Bigger than Ida. A cast of dozens. . .hundreds. . .thousands! Visit here on Tuesday morning to find out what the hyperbole is all about!

Wednesday, September 2, 2009

Nearly two years ago, I ran thisseriesonabunch of reference managers available in both commercial and open source models. Some things have changed since then, and others have not. OpenOffice.org Bibliographic has pretty much stagnated, Bibus has undergone incremental improvements, and Zotero has leap-frogged ahead to a function-rich 2.0 beta and survived a lawsuit from the makers of Endnote (which remains the commercial standard for reference management).

Today, a post at Bora Zivkovic's Blog Around the Clock higlights yet another new bibliographic offering, Mendeley. It is free, but not open source, and still in the beta stage, but it looks like it might offer some interface improvements over programs like Zotero and Endnote. Definitely worth following - do any of you readers have experience with Mendeley?

Wednesday, August 26, 2009

Darren Tanke, a technician at the Royal Tyrrell Museum of Paleontology, is probably one of the most knowledgeable people around when it comes to the history of paleontology in Alberta. I've known Darren for a number of years (and have co-authored several papers with him, including this one), and his enthusiasm for paleo lore is quite infectious. Stick around him for an hour or two, and you'll learn about the clues contained within quarry trash. . .discarded newspapers, plaster bits, sardine tins, and bottles are invaluable for identifying the original excavators of otherwise anonymous quarries. Many early paleontologists only kept the most minimal documentation, but thanks to Darren and his colleagues we now know the exact stratigraphic position for many important specimens from Dinosaur Provincial Park. This unglamorous service, a meld of archaeology, history, and paleontology, has done wonders for clarifying our understanding of Cretaceous ecosystems.

In the old days, vehicle access to places like Dinosaur Provincial Park was pretty darned difficult. In fact, many of the first expeditions were by boat, floating down the Red Deer River. Life is much easier for fossil collectors now. . .but in honor of these early expeditions, Darren is going to collect by boat once again! The Tyrrell's master carpenter, Perry Schopff, is presently working to recreate one of the AMNH's original scows. And come next summer, Darren and his crew of paleontologists will float in the footsteps of legends such as Barnum Brown - exactly 100 years after the first floating expedition.

In the spirit of open science, Darren and friends have put together a blog and Facebook group (search for "Dinosaur Hunting by Boat in Alberta, Canada") with all of the latest photos and updates. Here's to open science, and a successful field season in 2010!

Tuesday, August 25, 2009

Today, Victoria Arbour published a paper in PLoS ONEon ankylosaur tail club function, resulting from her M.Sc. thesis work at University of Alberta. As a quick reminder, ankylosaurs are those tank-like herbivorous dinosaurs, famous for having a big old lump of bone at the end of the tail (see picture at end of this post). Ms. Arbour estimated the impact force resulting from the tail clubs of several different ankylosaur specimens (belonging to the genera Euoplocephalus and Dyoplosaurus). The conclusion is that the largest ankylosars, but not smaller ones, could have generated enough force to crack the bones of an unlucky opponent. In other words. . .if the clubs weren't functional as weapons until adulthood, were the structures used for intraspecific combat, rather than defense against tyrannosaurs or other predators? There are clearly some great research projects in store along this line of inquiry! The paper is nice and detailed, with lots of math, figures, measurements, and other goodies clearly laid out for those who are so inclined.

So, go check out this new piece of dinosaur science! Because the work is published at the on-line, open access journal PLoS ONE, it is freely available. Furthermore, you can post comments on the paper at the journal site, rate the paper, and a whole host of other fun stuff. Do take advantage of these functions - it's a great way to contribute to the scientific process in a productive fashion.

This paper holds a special place in my heart, as the first manuscript that I took on after joining the PLoS ONE board of academic editors (this bit of information is identified on the up-front on the PLoS ONE website; not every journal has this level of editorial transparency!). Look for some more cool paleo papers in the very near future!

Wednesday, August 19, 2009

Recently, I highlighted the roles of mailing lists, social networking, and blogs in scientific discourse and discussion. Because I am so thoroughly grounded in the Internet age, I completely forgot to mention that old stand-by of scientific discourse, the Comment-And-Reply. Fortunately, the blogosphere has taken care of the issue for me!

First, refer to this simultaneously amusing and disturbing account of physicist Rick Trebino's experience trying to get a comment published on a paper bashing his work [PDF and the addendum PDF]. The issue at play concerns the sheer difficulty in correcting the literature when and if necessary. We're only seeing one side of the story here, but given the blatant idiocy of the anonymous journal's actions I am inclined to believe in the story's truth. Then, check out follow-up and commentary at Dynamics of Cats, Adventures in Ethics and Science, and Blog Around the Clock. Bora at BAC in particular highlights the roles that commenting functions at journals like PLoS ONE may play in streamlining scientific debate. Because these commenting functions are (hopefully) forever linked to the article itself, they may eventually supplant the blog and mailing list in this regard.

After saying all that, I should note that I had a very good experience recently with writing a comment on a recently published paper in Naturwissenschaften (not open access, sorry. . .). The journal was quite speedy in review and publication - the original article was published on March 10, our comment submitted on April 2, accepted with review on April 7, and published by May 7 (easier, of course, for a monthly publication with advance on-line publication). The authors of the paper upon which we were commenting were collegial in their published response, even though they disagreed with our critique. Never have I felt more keenly that "this is how science should work!"

Friday, August 14, 2009

﻿A few months ago, I decided that I needed a computer to take into the field. My primary laptop, a two-year old Dell Latitude DE1505 (which I love!) is steadily losing battery charge capacity. . .I'm lucky to get more than an hour out of it when unplugged. Because my primary field camp is relatively remote and without electricity, I needed something with a little more juice to it. Buying a new battery seemed a little expensive, especially for a laptop of that age (and I wouldn't gain that much in battery life anyhow). So, I started looking around for options.

I very quickly found the Asus Eee PC line as an interesting option. They're tiny, energy efficient, cheap, and run Linux easily. Who could ask for a better combination? So, I plunked down about $300 for the Asus Eee PC 901. . .I am writing the bulk of this blog post from my tent in a remote corner of Utah, if that is an indication of a worthwhile purchase! In this post, I'll discuss my experience using this little machine under paleontological conditions.

First, the physical characteristics of the Eee PC 901. It's really a netbook, which means small, small, small, measuring 8.8 inches in maximum width! This is great when you want something that's easily transportable, but the tiny keys on the keyboard take some getting used to. Additionally, many keys such as PageUp and PageDown are accessible only through a key combination (for instance, “Function” plus the “Up” arrow for PageUp) rather than as their own keys. After a little bit of practice, I got the hang of it. The track pad is small but adequate – for serious use, I'd probably plug in a regular mouse and keyboard, but it's more than enough for field use.

The screen is also small, but very legible. I find that when I'm typing in a word processor, particularly when reclining in my tent, it's helpful to zoom in a bit to get a good look at the text. Not unexpected for a netbook, again. The screen brightness is pretty good, although as with nearly any laptop it is tough to read in direct or bright indirect sun.

Now on to the nuts and bolts. Because I bought a Linux model, it came with a 20 gigabyte solid state drive (essentially, a USB stick for a hard drive). The solid state drive allows the computer to eke out every bit of battery life, because it doesn't have to keep a hard disk spun up all of the time. That said, 20 gigs isn't that much space these days, so I bought an 8 gig SD card for extra file capacity. The Eee PC has an SD card slot on the side, which is a major bonus!

The default operating system for the Eee PC is either Windows Vista (blech) or a custom build of Linux based on the Mandriva distribution. Open source paleontologist that I am, I went with the latter option. The factory Linux OS is adequate and intuitive, but I was frustrated by the difficulty in installing custom software or even updated packages of some key systems. I want OpenOffice.org 3.1, not 2.7! So, I installed a distribution called “Easy Peasy.” Despite (or perhaps because of) its cheesy name, “Easy Peasy” runs pretty much flawlessly on my machine. The desktop environment differs from Ubuntu in having nice large buttons on the desktop rather than a drop-down menu—a simplification, but a good one for something with a screen of this size. It's easy to install or upgrade applications (same method as with Ubuntu), and the default applications are comprehensive and up to date.

When within wi-fi range, the wireless card in my EeePC works flawlessly. In fact, I usually get better signal pick-up and connection reliability than the Windows or Mac users working alongside me (this is a hallmark of most Linux laptops I've worked with). Unfortunately, it does not seem to be particularly easy to turn off the wi-fi card with the default settings in Easy Peasy. So, I installed eee-control, a little utility that I highly, highly recommend for anyone using an EeePC. This fixed the problem quite elegantly! Unfortunately, I didn't find this piece of software until after I got back from the field.

I haven't completely run my battery down out in the field, but the battery life estimator indicates around 4.5 to 5 hours on a full charge. I suspect I could get longer life by turning off wi-fi (and I'll have to see how eee-control helps out in this regard), but this is still pretty darned good! I purchased a power inverter in order to charge the netbook as needed from our field truck's cigarette lighter. This setup has been working well.

In the field, I've been using my EeePC to keep track of the specimen field catalog as well as working on various writing projects (including this blog post) after hours in my tent. All told, the machine is more than adequate for these tasks. I'm not running my computer during the heat of the day, so I can't speak for its behavior at 100 degrees, and I am careful to store it away from any major sources of dust or grit. As mentioned above, it is tough to read anything on the screen under bright lighting conditions.

In the end, I would rate my Eee PC 901 a solid A-. The very portable size and long battery life for a good computing experience. The only things preventing me from issuing a completely glowing recommendation is the rather limited default Linux operating system (an easily rectified problem) and the initial problems with turning off the wi-fi card in Easy Peasy. I wouldn't recommend this as someone's primary computer (the tiny keyboard would probably give you hand cramps after awhile, and the processing speed and hard drive space are minimal for any real multimedia tasks or storage), but the affordable price makes the EeePC 901 a quite attractive option for a travel or field computer.

Friday, July 24, 2009

Sorry for the massive delay in posting - as many of my readers probably experience, summer is a busy time for fieldwork, catching up on research projects, and the like. In the morning, I'm heading into the field for the next three weeks. Upon my return, you can look forward to the following posts:

A full review of the Asus Eee PC 901 as an option for field paleontologists. I bought one a few months ago as an ultra-light travel laptop as well as a machine for the field. Its extended battery life (up to 8 hours under the most ideal conditions, allegedly) is particularly intriguing to me. . .will it hold up to the hype?

A look at how to use ImageJ for basic measurements from digital photographs, including lengths and angles.

More open source journal goodness, with a focus on one or two publications in particular.

And another link. . .an interesting piece of free software called paleoPhylo was just published in the latest issue of Paleobiology. It slices! It dices! It draws temporally-calibrated phylogenies using R!

Wednesday, July 15, 2009

Journal of Vertebrate Paleontology, as many readers of this blog know, is the flagship publication of the Society of Vertebrate Paleontology. Like the journals of many other small societies, JVP is a high-quality, largely volunteer effort. With the growth of SVP, the journal has grown too - from 422 published pages during its first year (1981) to 1,245 pages during 2008. This sort of expansion is not without its problems - how do you fit the increasing number of scientifically worthy submissions within the fixed-page format of a relatively expensive publication medium? Massive backlogs are bound to happen (and have, apparently). One option is to drastically increase the rejection rate of previously worthy papers - not necessarily a healthy option for the journal or the society as a whole (particularly for students and others not in the inner circles). Another tactic is to increase the number of pages per year, or the number of issues. For a society-funded journal, this is a very expensive proposition.

So, the Society of Vertebrate Paleontology has taken a compromise position - partnering with commercial publishing house Taylor & Francis Group. At the face of it, this seems to be a win-win situation. . .the number of issues will be bumped up to six issues per year, which will decrease the journal's backlog and allow more high-quality papers to be published. The society retains editorial control, gets a bunch of free color pages every year (no small chunk of cash saved here!), and will get a memoir issue every year too (also a major bonus - these things are very, very expensive to produce). Taylor & Francis also has an open access option for many of their journals (although it is unknown yet if JVP will have this available), which may be a step forward from the previously no-open-access-option of JVP.

This all seems like a Good Thing. So, why am I hesitant to completely cheer on the switch? My caution lies entirely with all of the uncertainties behind a switch to a big commercial publisher. The T&F Group seems to have much more restrictive policies on PDF distribution, for instance. . .in my quick look through their present journals, I didn't see any evidence for any journal that authors are allowed to purchase a PDF for a reasonable price that would legally allow posting of a copy on a personal or institutional website (as JVP presently does--something I really like about the journal). At best, authors get the concession of a free PDF for emailing purposes only. . .and only for up to 50 colleagues. There are days when I like to think more than 50 people might be interested in my research, but perhaps this is a fantasy. My hope is that something better has been negotiated for the society, but it is presently too early to tell. Furthermore, non-members of the society at non-subscribing institutions can look forward to paying $37/article (regardless of page count!) for PDF access. This is a step ahead of the previous situation (no easy way to get a PDF short of writing the author, assuming their contact information is still valid and the author is still alive), but a debatable improvement nonetheless.

All we have to go on right now is the press release. I am sure that many more details will be unveiled in the months leading up to the formal handover to Taylor & Francis. Some of my fears will be unfounded (I hope), and other unforeseen issues may rear their heads. At the very least, I will be keeping a close eye on further developments. If you publish in JVP or are thinking about doing so, and care about authors' rights, I encourage you to remain vigilant too.

Thursday, July 2, 2009

The Cretaceous of Gondwana - the formerly connected southern landmasses of Antarctica, Australia, South America, Africa, India, Madagascar, and Arabia - is a sticky problem. The terrestrial fossil record is spotty at best in most locations, and tremendous geographic and temporal gaps remain. As a consequence, there is considerable debate about the sequence of the tectonic breakup of Gondwana and even the very identity and relationships of some of its dinosaurs and other Mesozoic beasts. Once in a great while, some intrepid field paleontologists take a chance and make discoveries that move our knowledge ahead by leaps and bounds. Areas of Gondwana such as Madagascar and Argentina have had fossils rolling out of the Cretaceous hills, doing wonders for paleontological knowledge. Today, a new paper in PLoS ONEhas done such a thing for Australia.

Historically, paleontologists working in the Cretaceous of Oz have had to make do with pretty fragmentary material. With the exception of Muttaburrasaurus(a plant eating ornithopod known from reasonably complete skulls and skeletal material) and Minmi(an armored ankylosaur known from a relatively complete skeleton), most of the other named taxa from this time are known only from scrappy elements (e.g., Kakura, a theropod known from an isolated, opalized tibia). This poor fossil record has resulted in some odd, and highly unlikely, claims. For instance, it has been suggested that ceratopsians (otherwise known only from the northern hemisphere) lived in Australia (based on isolated ulnae that admittedly do look rather ceratopsian - although other assignments haven't necessarily been ruled out effectively), and that Allosaurus (a late Jurassic theropod from North America) survived into the early Cretaceous here. When it comes to the meat-eating theropods and the long-necked sauropods, the material is pretty frustrating. Without better specimens, it's virtually impossible to know how Australia's animals compared to those elsewhere!

For this reason, the new paper is so very important. A team of paleontologists from the Queensland Museum and the Australian Age of Dinosaurs Museum of Natural History here describe three completely new dinosaur species. Two are sauropods, the third is a theropod, and all come from the Winton Formation of Queensland. The portion of the Winton Formation hosting the dinosaurs is estimated as late Albian in age (based on fossil pollen, an important criterion in the absence of radiometric dates), or roughly 100 million years old.

The two sauropods belong to a group called titanosaurs. Titanosaurs were the dominant sauropods of the Cretaceous, with a virtually global distribution. Diamantinasaurus matildae (the sauropod at the top in the illustration, charmingly named after "Waltzing Matilda") and Wintonotitan wattsi (bottom) are both known from partial skeletons, whose owners might have measured 50 feet in total length (~14.8 m) when alive. Unfortunately, the phylogenetic position of the two animals is somewhat uncertain. The authors chose to put the animals into two very different datasets for their cladistic analysis (in terms of characters and taxon selection), so it's tough to know where the things actually fall out. It would be informative to merge the two datasets as much as possible and see how that affects tree topology. The incongruent trees also complicate any biogeographic conclusions that might be drawn. Regardless, it looks like Wintonotitan is a relatively basal titanosauriform (what some folks might call "primitive"), and Diamantinasaurus falls out within a group called Lithostratia, close to or within the saltasaurids (many of these animals are well-known for the armor studding their backs).

There is a slim possibility that one or both new species of sauropod are synonymous with Austrosaurus mckillopi, a taxon based on poorly preserved, incomplete vertebrae from a roughly contemporaneous formation. There is some overlap with Wintonotitan, but the vertebrae from the two animals are apparently pretty different. Diamantinasaurus doesn't preserve any vertebrae, so we can't directly compare it with Austrosaurus. But because the type of Austrosaurus is so incomplete, it might be safely ignored as a nomen dubium. I'll leave it to the sauropod experts to decide that!

Our third beast is a theropod (meat-eating dinosaur) named Australovenator wintonensis. It was perhaps a third of the body length of the two sauropods and is represented by a partial skeleton including a complete hindlimb, partial forelimbs, and a portion of the lower jaw. For Australian theropods, this is simply dumbfounding material (remember Kakura, only known from a fragmentary leg bone?). Heck, for theropods anywhere this is pretty darned good. Australovenator falls out as an allosauroid (a pretty common group of predators from the Jurassic and Cretaceous) just outside of carcharodontosaurids. With Australovenator thrown into the mix, allosauroids had a nearly global distribution.

Open Access NerdinessThis paper is a fantastic example of the real benefits of an on-line, open access journal like PLoS ONE. Without page limitations, the authors were allowed to truly monograph the heck out of the bones. Virtually every element is illustrated from multiple angles (with high resolution photos downloadable from the website!) and accompanied by thorough text descriptions and measurements. The editors of most journals would freak out over such a "waste" of precious space - but I have a feeling that future researchers are going to thank the authors for their thoroughness. As a PDF, the paper weighs in at 51 pages - and this doesn't include the supplementary information!

The authors (perhaps at the editors' behest) also make very explicit statements about the nomenclatural availability of the names, a direct result of the Darwinius fallout. Hopefully this will satisfy the requirements ICZN.

On the rather nitpicky side, I would note that the minimal post-processing of the manuscripts employed by PLoS ONE shows up here and there. For instance, the term "phalange" is used as the singular instead of the correct "phalanx" (one of my few pet peeves), among a few other oddities. These are rather minor bones to pick in an otherwise weighty manuscript.

As always, if you have something to say, post a comment here and then go provide your comments, notes, and ratings of the article at the PLoS ONE website.

The Bottom LineSo what's so important about this paper? Well, we finally have good sauropod material from the Cretaceous of Australia, and an excellent theropod specimen to go along with it. No doubt--these specimens are going to be critical for future studies on the evolution and biogeography of both groups, as well as greatly filling in our understanding of Australia's geological past. It is not an exaggeration to say that Australian dinosaur paleontology has taken a quantum leap forward!

Dinosaurs of the Winton Formation, including Wintonotitan (left), Diamantinasaurus (middle), and Australoraptor (right). This and the above images are modified from the originals by T. Tischler (citation below), under a Creative Commons Attribution license.

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Ramblings on the role of open source software and open access publishing in paleontology, the latest and sometimes not-so-greatest ways in which we reconstruct the past, and the occasional bits of career advice and paleo news.

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This is a personal weblog, and the opinions expressed here represent my own and not those of my employer or any other organization with which I am associated. Although I strive for accurate information, please be aware that the advice offered here is "as is," with no claims or guarantees that it will work for you. Hey, I'm just a paleontologist.